Marine heatwaves (MHWs) are intensifying globally, yet their risks and impacts to fish and benthic communities remains poorly resolved. Mesophotic fish communities (30-150m) are likely to face increased stress from MHWs as they occur at depths where MHWs often reach their highest intensity. Despite this, community changes and MHW impacts are still uncertain and variable. Using satellite SST data and a 26-year high resolution ocean hindcast model, we assessed the risk of MHWs to mesophotic communities using key MHW metrics of frequency, duration, and intensity. Furthermore, secondary modulators of seasonality and long-term warming were included to heighten risk in regions with strong seasonal and interannual cycles, where MHWs occurring during the warmest periods may pose greater thermal stress to mesophotic communities. The results revealed a significant divergence between surface and benthic MHW risk patterns along the east coast of Australia, where surface-based MHW metrics poorly represent the conditions experienced by deeper fish communities. Furthermore, regional contrasts demonstrate that no single spatial pattern characterises risk with differences across the EAC jet and the separation zone, where surface-based risk fails to represent subsurface dynamics. This challenges our current use of SST metrics for management of these communities and highlights the importance of a depth resolved approach to modelling their future distributions and responses to MHW events.